Ion-beam sculpting at nanometre length scales

Local solid-state modification of nanopore surface charges

Over the last decade, nanopores have emerged as a new and interesting tool for the study of biological macromolecules like proteins and DNA. While biological pores, especially alpha-haemolysin, have been promising for the detection of DNA, their poor chemical stability limits their use. For this reason, researchers are trying to mimic their behaviour using more stable, solid-state nanopores. The most successful tools to fabricate such nanopores use high energy electron or ions beams to drill or reshape holes in very thin membranes. While the resolution of these methods can be very good, they require tools that are not commonly available and tend to damage and charge the nanopore surface. In this work, we show nanopores that have been fabricated using standard micromachining techniques together with EBID, and present a simple model that is used to estimate the surface charge. The results show that EBID with a silicon oxide precursor can be used to tune the nanopore surface and that the surface charge is stable over a wide range of concentrations.

Detection of DNA hybridizations using solid-state nanopores

We report an experimental study of using DNA translocation through solid-state nanopores to detect the sequential arrangement of two double-stranded 12-mer hybridization segments on a single-stranded DNA molecule. The sample DNA is a trimer molecule formed by hybridizing three single-stranded oligonucleotides. A polystyrene bead is attached to the end of the trimer DNA, providing a mechanism in slowing down the translocation and suppressing the thermal diffusion, thereby allowing the detection of short features of DNA by standard patch-clamp electronics. The electrical signature of the translocation of a trimer molecule through a nanopore has been identified successfully in the temporal traces of ionic current. The results reported here represent the first successful attempt in using a solid-state nanopore as an ionic scanning device in resolving individual hybridization segments (or 'probes') on a DNA molecule.

Programmable growth of branched silicon nanowires using a focused ion beam

Although significant progress has been made in being able to spatially define the position of material layers in vapor-liquid-solid (VLS) grown nanowires, less work has been carried out in deterministically defining the positions of nanowire branching points to facilitate more complicated structures beyond simple 1D wires. Work to date has focused on the growth of randomly branched nanowire structures. Here we develop a means for programmably designating nanowire branching points by means of focused ion beam-defined VLS catalytic points. This technique is repeatable without losing fidelity allowing multiple rounds of branching point definition followed by branch growth resulting in complex structures. The single crystal nature of this approach allows us to describe resulting structures with linear combinations of base vectors in three-dimensional (3D) space. Finally, by etching the resulting 3D defined wire structures branched nanotubes were fabricated with interconnected nanochannels inside. We believe that the techniques developed here should comprise a useful tool for extending linear VLS nanowire growth to generalized 3D wire structures.

DNA translocation through graphene nanopores

We report on DNA translocations through nanopores created in graphene membranes. Devices consist of 1-5 nm thick graphene membranes with electron-beam sculpted nanopores from 5 to 10 nm in diameter. Due to the thin nature of the graphene membranes, we observe larger blocked currents than for traditional solid-state nanopores. However, ionic current noise levels are several orders of magnitude larger than those for silicon nitride nanopores. These fluctuations are reduced with the atomic-layer deposition of 5 nm of titanium dioxide over the device. Unlike traditional solid-state nanopore materials that are insulating, graphene is an excellent electrical conductor. Use of graphene as a membrane material opens the door to a new class of nanopore devices in which electronic sensing and control are performed directly at the pore.

Single-molecule observation of protein adsorption onto an inorganic surface

Understanding the interactions between silicon-based materials and proteins from the bloodstream is of key importance in a myriad of realms, such as the design of nanofluidic devices and functional biomaterials, biosensors, and biomedical molecular diagnosis. By using nanopores fabricated in 20 nm-thin silicon nitride membranes and highly sensitive electrical recordings, we show single-molecule observation of nonspecific protein adsorption onto an inorganic surface. A transmembrane potential was applied across a single nanopore-containing membrane immersed into an electrolyte-filled chamber. Through the current fluctuations measured across the nanopore, we detected long-lived captures of bovine serum albumin (BSA), a major multifunctional protein present in the circulatory system. Based upon single-molecule electrical signatures observed in this work, we judge that the bindings of BSA to the nitride surface occurred in two distinct orientations. With some adaptation and further experimentation, this approach, applied on a parallel array of synthetic nanopores, holds potential for use in methodical quantitative studies of protein adsorption onto inorganic surfaces.

Stochastic nanopore sensors for the detection of terrorist agents: current status and challenges

Nanopore stochastic sensor works by monitoring the ionic current modulations induced by the passage of analytes of interest through a single pore, which can be obtained from a biological ion channel by self-assembly or artificially fabricated in a solid-state membrane. In this minireview, we overview the use of biological nanopores and artificial nanopores for the detection of terrorist agents including explosives, organophosphorus nerve agents, nitrogen mustards, organoarsenic compounds, toxins, and viruses. We also discuss the current challenge in the development of deployable nanopore sensors for real-world applications.

Applications of biological pores in nanomedicine, sensing, and nanoelectronics

Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated - often regulated - functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics.

Polymer translocation into a fluidic channel through a nanopore

Using two-dimensional Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a fluidic channel with diameter R through a nanopore under a driving force F . Due to the crowding effect induced by the partially translocated monomers, the translocation dynamics is significantly altered in comparison to an unconfined environment, namely, we observe a nonuniversal dependence of the translocation time τ on the chain length N . τ initially decreases rapidly and then saturates with increasing R , and a dependence of the scaling exponent α of τ with N on the channel width R is observed. The otherwise inverse linear scaling of τ with F breaks down and we observe a minimum of α as a function of F . These behaviors are interpreted in terms of the waiting time of an individual segment passing through the pore during translocation.

DNA translocation through an array of kinked nanopores

Synthetic solid-state nanopores are being intensively investigated as single-molecule sensors for detection and characterization of DNA, RNA and proteins. This field has been inspired by the exquisite selectivity and flux demonstrated by natural biological channels and the dream of emulating these behaviours in more robust synthetic materials that are more readily integrated into practical devices. So far, the guided etching of polymer films, focused ion-beam sculpting, and electron-beam lithography and tuning of silicon nitride membranes have emerged as three promising approaches to define synthetic solid-state pores with sub-nanometre resolution. These procedures have in common the formation of nominally cylindrical or conical pores aligned normal to the membrane surface. Here we report the formation of 'kinked' silica nanopores, using evaporation-induced self-assembly, and their further tuning and chemical derivatization using atomic-layer deposition. Compared with 'straight through' proteinaceous nanopores of comparable dimensions, kinked nanopores exhibit up to fivefold reduction in translocation velocity, which has been identified as one of the critical issues in DNA sequencing. Additionally, we demonstrate an efficient two-step approach to create a nanopore array exhibiting nearly perfect selectivity for ssDNA over dsDNA. We show that a coarse-grained drift-diffusion theory with a sawtooth-like potential can reasonably describe the velocity and translocation time of DNA through the pore. By control of pore size, length and shape, we capture the main functional behaviours of protein pores in our solid-state nanopore system.

Ion transport in nanofluidic funnels

We report fabrication of nanofluidic channels with asymmetric features (e.g., funnels) that were cast in high modulus poly(dimethylsiloxane) and had well-defined geometries and dimensions. Masters used to cast the funnels were written in the negative tone resist SU-8 by electron beam lithography. Replicated funnels had taper angles of 5, 10, and 20 degrees and were 80 nm wide at the tip, 1 microm wide at the base, and 120 nm deep. The planar format permitted easy coupling of the funnels to microfluidic channels and simultaneous electrical and optical characterization of ion transport. All three designs rectified ion current, and the 5 degrees funnel exhibited the highest rectification ratio. Fluorescence measurements at the funnel base showed that an anionic probe was enriched and depleted in the high and low conductance states, respectively.

Nanopore analysis of nucleic acids bound to exonucleases and polymerases

When a voltage is imposed across a thin membrane containing a nanoscopic pore, the electric field generated within the pore captures linear ionized polymers, such as nucleic acids, that are present in the solution bathing the pore. The nucleic acid molecule transiently blocks ionic current as it is translocated through the pore, and modulations of the current provide information about the structure and dynamic motion of the molecule. Altering the imposed voltage allows movement of the DNA molecule in the pore to be controlled. If a DNA-processing enzyme such as an exonuclease or polymerase is present, the enzyme-DNA complex is also drawn to the pore, and further modulations of the ionic current reflect enzyme function at the single-molecule level on millisecond timescales. The combined enzymatic and voltage control of a DNA molecule in the nanopore can be used to sequence the DNA.

Fabrication of metallized nanopores in silicon nitride membranes for single-molecule sensing

The fabrication and characterization of a metallized nanopore structure for the sensing of single molecules is described. Pores of varying diameters (>10 nm) are patterned into free-standing silicon nitride membranes by electron-beam lithography and reactive ion etching. Structural characterization by transmission electron microscopy (TEM) and tomography reveals a conical pore shape with a 40 degrees aperture. Metal films of Ti/Au are vapor deposited and the pore shape and shrinking are studied as a function of evaporated film thickness. TEM tomography analysis confirms metalization of the inner pore walls as well as conservation of the conical pore shape. In electrical measurements of the transpore current in aqueous electrolyte solution, the pores feature very low noise. The applicability of the metallized pores for stochastic sensing is demonstrated in real-time translocation experiments of single lambda-DNA molecules. We observe exceptionally long-lasting current blockades with a fine structure of distinct current levels, suggesting an attractive interaction between the DNA and the PEGylated metallic pore walls.

Molecular diagnostics for personal medicine using a nanopore

Semiconductor nanotechnology has created the ultimate analytical tool: a nanopore with single molecule sensitivity. This tool offers the intriguing possibility of high-throughput, low cost sequencing of DNA with the absolute minimum of material and preprocessing. The exquisite single molecule sensitivity obviates the need for costly and error-prone procedures like polymerase chain reaction amplification. Instead, nanopore sequencing relies on the electric signal that develops when a DNA molecule translocates through a pore in a membrane. If each base pair has a characteristic electrical signature, then ostensibly a pore could be used to analyze the sequence by reporting all of the signatures in a single read without resorting to multiple DNA copies. The potential for a long read length combined with high translocation velocity should make resequencing inexpensive and allow for haplotyping and methylation profiling in a chromosome.

Nanopore fabrication in amorphous Si: Viscous flow model and comparison to experiment

Nanopores fabricated in free-standing amorphous silicon thin films were observed to close under 3 keV argon ion irradiation. The closing rate, measured in situ, exhibited a memory effect: at the same instantaneous radius, pores that started larger close more slowly. An ion-stimulated viscous flow model is developed and solved in both a simple analytical approximation for the small-deformation limit and in a finite element solution for large deformations. The finite-element solution exhibits surprising changes in cross-section morphology, which may be extremely valuable for single biomolecule detection, and are untested experimentally. The finite-element solution reproduces the shape of the measured nanopore radius versus fluence behavior and the sign and magnitude of the measured memory effect. We discuss aspects of the experimental data not reproduced by the model, and successes and failures of the competing adatom diffusion model.

Macroporous Semiconductors

Pores in single crystalline semiconductors come in many forms (e.g., pore sizes from 2 nm to > 10 µm; morphologies from perfect pore crystal to fractal) and exhibit many unique properties directly or as nanocompounds if the pores are filled. The various kinds of pores obtained in semiconductors like Ge, Si, III-V, and II-VI compound semiconductors are systematically reviewed, emphasizing macropores. Essentials of pore formation mechanisms will be discussed, focusing on differences and some open questions but in particular on common properties. Possible applications of porous semiconductors, including for example high explosives, high efficiency electrodes for Li ion batteries, drug delivery systems, solar cells, thermoelectric elements and many novel electronic, optical or sensor devices, will be introduced and discussed.

Mapping the variation of the translocation α scaling exponent with nanopore width

The unbiased translocation of a coarse-grained polymer through a nanopore is investigated via Langevin dynamics simulations for polymers ranging from N=19 to 299 monomers in length and pore widths r p ranging from 1 to 10 times the monomer diameter. The exponent α derived from the scaling of the translocation time τ with respect to the molecular weight N is found to be heavily dependent on r p and increases from a value of 2.2 for r p=1.0 up to a saturation value of 3. The details of the translocation process also reveal that the average number of monomers in the pore [n p] not only varies as translocation proceeds but that for any polymer where the radius of gyration is greater than the radius of the available pore width, [n p] decreases with increasing N. Using these data to rescale the results according to a blob picture, the results retain sensitivity on the pore geometry as α varies from 2.2 to 2.65--a range which covers all results reported in previous studies.

Nanopore Sequencing: Electrical Measurements of the Code of Life

Sequencing a single molecule of deoxyribonucleic acid (DNA) using a nanopore is a revolutionary concept because it combines the potential for long read lengths (>5 kbp) with high speed (1 bp/10 ns), while obviating the need for costly amplification procedures due to the exquisite single molecule sensitivity. The prospects for implementing this concept seem bright. The cost savings from the removal of required reagents, coupled with the speed of nanopore sequencing places the $1000 genome within grasp. However, challenges remain: high fidelity reads demand stringent control over both the molecular configuration in the pore and the translocation kinetics. The molecular configuration determines how the ions passing through the pore come into contact with the nucleotides, while the translocation kinetics affect the time interval in which the same nucleotides are held in the constriction as the data is acquired. Proteins like α-hemolysin and its mutants offer exquisitely precise self-assembled nanopores and have demonstrated the facility for discriminating individual nucleotides, but it is currently difficult to design protein structure ab initio, which frustrates tailoring a pore for sequencing genomic DNA. Nanopores in solid-state membranes have been proposed as an alternative because of the flexibility in fabrication and ease of integration into a sequencing platform. Preliminary results have shown that with careful control of the dimensions of the pore and the shape of the electric field, control of DNA translocation through the pore is possible. Furthermore, discrimination between different base pairs of DNA may be feasible. Thus, a nanopore promises inexpensive, reliable, high-throughput sequencing, which could thrust genomic science into personal medicine.

Bacterial nanofluidic structures for medicine and engineering

Bacteria are microscopic, single-celled organisms that utilize a variety of nanofluidic structures. One of the best known and widely used nanofluidic structures that are derived from bacteria is the alpha-hemolysin pore. This pore, which self-assembles in lipid bilayers, has been used for a wide variety of sensing applications, most notably, DNA sensing. Synthetic pores drilled in a wide variety of materials, such as silicon nitride and polymers have been developed that use inspiration from the alpha-hemolysin pore. Higher-aspect-ratio nanofluidic structures, akin to nanotubes, are also synthesized by bacteria. Examples of such structures include those that are associated with bacterial transport apparatus, such as pili, and are used by bacteria to facilitate the transfer of genetic material from one bacterium to another. Flagella, and its associated structures, such as the rod and hook, are also tubular nanostructures, through which the protein, flagellin, travels to assemble the flagellum. Genetic engineering allows for the creation of modified bacterial nanopores and nanotubes that can be used for a variety of medical and engineering purposes.

DNA Sensing using Nano-crystalline Surface Enhanced Al(2)O(3) Nanopore Sensors

A new solid-state, Al(2)O(3) nanopore sensor with enhanced surface properties for the real-time detection and analysis of individual DNA molecules is reported. Nanopore formation using electron beam based decomposition transformed the local nanostructure and morphology of the pore from an amorphous, stoichiometric structure (O to Al ratio of 1.5) to a hetero-phase crystalline network, deficient in O (O to Al ratio of ~0.6). Direct metallization of the pore region was observed during irradiation, thereby permitting the potential fabrication of nano-scale metallic contacts in the pore region with potential application to nanopore-based DNA sequencing. Dose dependent phase transformations to purely γ and/or α-phase nanocrystallites were also observed during pore formation allowing for surface charge engineering at the nanopore/fluid interface. DNA transport studies revealed an order of magnitude reduction in translocation velocities relative to alternate solid-state architectures, accredited to high surface charge density and the nucleation of charged nanocrystalline domains. The unique surface properties of Al(2)O(3) nanopore sensors makes them ideal for the detection and analysis of ssDNA, dsDNA, RNA secondary structures and small proteins. These nano-scale sensors may also serve as a useful tool in studying the mechanisms driving biological processes including DNA-protein interactions and enzyme activity at the single molecule level.

Nanofluidic technology for biomolecule applications: a critical review

In this review, we present nanofluidic phenomena, particularly as they relate to applications involving analysis of biomolecules within nanofabricated devices. The relevant length scales and physical phenomena that govern biomolecule transport and manipulation within nanofabricated nanofluidic devices are reviewed, the advantages of nanofabricated devices are presented, and relevant applications are cited. Characteristic length scales include the Debye length, the Van der Waals radius, the action distance of hydrogen bonding, the slip length, and macromolecular dimensions. On the basis of the characteristic lengths and related nanofluidic phenomena, a nanofluidic toolbox will be assembled. Nanofluidic phenomena that affect biomolecule behavior within such devices can include ion depletion and enrichment, modified velocity and mobility, permselectivity, steric hindrance, entropy, adsorption, and hydrodynamic interaction. The complex interactions and coupled physics of such phenomena allow for many applications, including biomolecule separation, concentration, reaction/hybridization, sequencing (in the case of DNA) and detection. Examples of devices for such applications will be presented, followed by a discussion of near-term challenges and future thoughts for the field.

DNA-functionalized solid state nanopore for biosensing

The possible use of nanopores for single DNA molecules biosensing has been demonstrated, but much remains to do in order to develop advanced engineered devices with enhanced stability, and controlled geometry and surface properties. Here we present morphological and electrical characterization of solid state silicon nitride nanopores fabricated by focused ion beam direct milling and chemically functionalized by probe oligonucleotides, with the final aim of developing a versatile tool for biosensing and gene expression profiling.

Probing single nanometer-scale pores with polymeric molecular rulers

We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus alpha-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the alpha-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based "molecular rulers" may prove useful in deducing the structures of nanometer-scale pores in general.

Deciphering ionic current signatures of DNA transport through a nanopore

Within just a decade from the pioneering work demonstrating the utility of nanopores for molecular sensing, nanopores have emerged as versatile systems for single-molecule manipulation and analysis. In a typical setup, a gradient of the electrostatic potential captures charged solutes from the solution and forces them to move through a single nanopore, across an otherwise impermeable membrane. The ionic current blockades resulting from the presence of a solute in a nanopore can reveal the type of the solute, for example, the nucleotide makeup of a DNA strand. Despite great success, the microscopic mechanisms underlying the functionality of such stochastic sensors remain largely unknown, as it is not currently possible to characterize the microscopic conformations of single biomolecules directly in a nanopore and thereby unequivocally establish the causal relationship between the observables and the microscopic events. Such a relationship can be determined using molecular dynamics-a computational method that can accurately predict the time evolution of a molecular system starting from a given microscopic state. This article describes recent applications of this method to the process of DNA transport through biological and synthetic nanopores.

Eliminating the limiting-current phenomenon by geometric field focusing into nanopores and nanoslots

A peculiar and undesirable current-voltage characteristic of nanoporous membranes is that it exhibits a voltage window with a near-constant limiting-current density when bulk ions near one surface of the membrane are depleted. We show both theoretically and experimentally that this interval disappears for an isolated circular nanopore (or narrow nanoslot) because radial field focusing at the pore entrance enhances the depletion effect and drives an ejecting hydrodynamic vortex pair that amplifies ion flux into the nanopore. This vortex pair is distinct from the vortex arrays that appear in front of a wide nanoslot or a nanoporous membrane with small inter-nanopore separation. It hence suggests that an optimal pore radius/separation ratio exists for maximum current density across a membrane.

Aptamer-encoded nanopore for ultrasensitive detection of bioterrorist agent ricin at single-molecule resolution

The molecular-scale pore structure, called nanopore, can be formed from protein ion channels by genetic engineering or fabricated on solid substrates using fashion nanotechnology. Target molecules in interaction with the functionalized lumen of nanopore, can produce characteristic changes in the pore conductance, which act as fingerprints, allowing us to identify single molecules and simultaneously quantify each target species in the mixture. Nanopore sensors have been created for tremendous biomedical detections, with targets ranging from metal ions, drug compounds and cellular second messengers, to proteins and DNAs. Here we will review our recent discoveries with a lab-in-hand glass nanopore: single-molecule discrimination of chiral enantiomers with a trapped cyclodextrin, and sensing of bioterrorist agent ricin.

Controlling nanopore size, shape and stability

Solid-state nanopores are considered a promising tool for the study of biological polymers such as DNA and RNA, due largely to their flexibility in size, potential in device integration and robustness. Here, we show that the precise shape of small nanopores (approximately 5 nm diameter in 20 nm SiN membranes) can be controlled by using transmission electron microscope (TEM) beams of different sizes. However, when some of these small nanopores are immersed in an aqueous solution, their resistance is observed to decrease over time. By comparing nanopores of different shapes using (scanning) TEM both before and after immersion in aqueous solution, we demonstrate that the stability of small nanopores is related to their three-dimensional geometry, which depends on the TEM beam size employed during pore fabrication. Optimal stability is obtained using a TEM beam size of approximately the same size as the intended nanopore diameter. In addition, we show that thermal oxidation can serve as a means to independently control nanopore size following TEM fabrication. These observations provide key guidelines for the fabrication of stable solid-state nanopores on the scale of nucleic acids and small proteins.

Single molecule sensing by nanopores and nanopore devices

Molecular-scale pore structures, called nanopores, can be assembled by protein ion channels through genetic engineering or be artificially fabricated on solid substrates using fashion nanotechnology. When target molecules interact with the functionalized lumen of a nanopore, they characteristically block the ion pathway. The resulting conductance changes allow for identification of single molecules and quantification of target species in the mixture. In this review, we first overview nanopore-based sensory techniques that have been created for the detection of myriad biomedical targets, from metal ions, drug compounds, and cellular second messengers to proteins and DNA. Then we introduce our recent discoveries in nanopore single molecule detection: (1) using the protein nanopore to study folding/unfolding of the G-quadruplex aptamer; (2) creating a portable and durable biochip that is integrated with a single-protein pore sensor (this chip is compared with recently developed protein pore sensors based on stabilized bilayers on glass nanopore membranes and droplet interface bilayer); and (3) creating a glass nanopore-terminated probe for single-molecule DNA detection, chiral enantiomer discrimination, and identification of the bioterrorist agent ricin with an aptamer-encoded nanopore.

Data analysis of translocation events in nanopore experiments

Nanopores have become important tools for single molecule experiments, where information about the properties of DNA/RNA or proteins is inferred from current pulses elicited by individual molecules as they traverse a single pore. However, because of necessary electronic filters employed in the measurement technique, the extraction of meaningful information from short pulses is limited. This restricts the use of nanopores for the investigation of small molecules which cross the pore rapidly. Here we present a method which significantly improves the accuracy of the analysis of noise-filtered current pulses. We introduce improved criteria to measure the pulse width and propose a method to evaluate the pulse height from the falling edge of the pulse, which renders the identification of a pulse plateau unnecessary. The new methods are compared to conventional routines and validated by analyzing representative current pulses as well as experimental protein translocation data. It is demonstrated that the pulse properties can be recovered with satisfying accuracy beyond the usual limitations of Bessel filters, i.e., from pulses featuring a width of merely 0.3f(c)(-1) (f(c) being the filter cutoff frequency).

Rapid sequencing of individual DNA molecules in graphene nanogaps

I propose a technique for reading the base sequence of a single DNA molecule using a graphene nanogap to read the DNA's transverse conductance. Because graphene is a single atom thick, single-base resolution of the conductance is readily obtained. The nonlinear current-voltage characteristic is used to determine the base type independent of nanogap-width variations that cause the current to change by 5 orders of magnitude. The expected sequencing error rate is 0% up to a nanogap width of 1.6 nm.

Nanopores in solid-state membranes engineered for single molecule detection

A nanopore is an analytical tool with single molecule sensitivity. For detection, a nanopore relies on the electrical signal that develops when a molecule translocates through it. However, the detection sensitivity can be adversely affected by noise and the frequency response. Here, we report measurements of the frequency and noise performance of nanopores </=8 nm in diameter in membranes compatible with semiconductor processing. We find that both the high frequency and noise performance are compromised by parasitic capacitances. From the frequency response we extract the parameters of lumped element models motivated by the physical structure that elucidates the parasitics, and then we explore four strategies for improving the electrical performance. We reduce the parasitic membrane capacitances using: (1) thick Si(3)N(4) membranes; (2) miniaturized composite membranes consisting of Si(3)N(4) and polyimide; (3) miniaturized membranes formed from metal-oxide-semiconductor (MOS) capacitors; and (4) capacitance compensation through external circuitry, which has been used successfully for patch clamping. While capacitance compensation provides a vast improvement in the high frequency performance, mitigation of the parasitic capacitance through miniaturization offers the most promising route to high fidelity electrical discrimination of single molecules.

Electroosmotic flow can generate ion current rectification in nano- and micropores

This paper introduces a strategy for generating ion current rectification through nano- and micropores. This method generates ion current rectification by electroosmotic-driven flow of liquids of varying viscosity (and hence varying conductance) into or out of the narrowest constriction of a pore. The magnitude of current rectification was described by a rectification factor, R(f), which is defined by the ratio of the current measured at a positive voltage divided by the current measured at a negative voltage. This method achieved rectification factors in the range of 5-15 using pores with diameters ranging from 10 nm to 2.2 microm. These R(f) values are similar to the rectification factors reported in other nanopore-based methods that did not employ segmented surface charges. Interestingly, this work showed that in cylindrical nanopores with diameters of 10 nm and a length of at least 275 nm, electroosmotic flow was present and could generate ion current rectification. Unlike previous methods for generating ion current rectification that require nanopores with diameters comparable to the Debye length, this work demonstrated ion current rectification in micropores with diameters 500 times larger than the Debye length. Thus this method extends the concept of fluidic diodes to the micropore range. Several experiments designed to alter or remove electroosmotic flow through the pore demonstrated that electroosmotic flow was required for the mode of ion current rectification reported here. Consequently, the magnitude of current rectification could be used to indicate the presence of electroosmotic flow and the breakdown of electroosmotic flow with decreasing ionic strength and hence increasing electric double layer overlap inside nanopores.

Detection of local protein structures along DNA using solid-state nanopores

Nanopores have been successfully employed as a new tool to rapidly detect single biopolymers, in particular DNA. When a molecule is driven through a nanopore by an externally applied electric field, it causes a characteristic temporary change in the trans-pore current. Here, we examine the translocation of DNA with discrete patches of the DNA-repair protein RecA attached along its length. Using the fact that RecA-coated DNA and bare DNA yield very different current-blockade signatures, we demonstrate that it is possible to map the locations of the proteins along the length of a single molecule using a solid-state nanopore. This is achieved at high speed and without any staining. We currently obtain a spatial resolution of about 8 nm, or 5 RecA proteins binding to 15 base pairs of DNA, and we discuss possible extensions to single protein resolution. The results are a crucial first step toward genomic screening, as they demonstrate the feasibility of reading off information along DNA at high resolution with a solid-state nanopore.

Micropore and nanopore fabrication in hollow antiresonant reflecting optical waveguides

We demonstrate the fabrication of micropore and nanopore features in hollow antiresonant reflecting optical waveguides to create an electrical and optical analysis platform that can size select and detect a single nanoparticle. Micropores (4 μm diameter) are reactive-ion etched through the top SiO(2) and SiN layers of the waveguides, leaving a thin SiN membrane above the hollow core. Nanopores are formed in the SiN membranes using a focused ion-beam etch process that provides control over the pore size. Openings as small as 20 nm in diameter are created. Optical loss measurements indicate that micropores did not significantly alter the loss along the waveguide.

Translocation of single-stranded DNA through single-walled carbon nanotubes

We report the fabrication of devices in which one single-walled carbon nanotube spans a barrier between two fluid reservoirs, enabling direct electrical measurement of ion transport through the tube. A fraction of the tubes pass anomalously high ionic currents. Electrophoretic transport of small single-stranded DNA oligomers through these tubes is marked by large transient increases in ion current and was confirmed by polymerase chain reaction analysis. Each current pulse contains about 10(7) charges, an enormous amplification of the translocated charge. Carbon nanotubes simplify the construction of nanopores, permit new types of electrical measurements, and may open avenues for control of DNA translocation.

Scanning probe and nanopore DNA sequencing: core techniques and possibilities

We provide an overview of the current state of research towards DNA sequencing using nanopore and scanning probe techniques. Additionally, we provide methods for the creation of two key experimental platforms for studies relating to nanopore and scanning probe DNA studies: a synthetic nanopore apparatus and an atomically flat conductive substrate with stretched DNA molecules.

Direct fabrication of nanopores in a metal foil using focused ion beam with in situ measurements of the penetrating ion beam current

A through hole with a diameter less than 100 nm was fabricated in an Ag foil using only a focused ion beam (FIB) system and in situ measurements of the penetrating ion beam. During the drilling of the foil by a FIB of Ga(+) ions, the transmitted part of the beam was measured with an electrode mounted on the back face of the foil. When the beam current penetrating through the nanopore reached a certain value, irradiation was stopped and the area of the created aperture was measured with a scanning electron microscope. The resulting area was correlated with the current of the penetrating ion beam. This suggests that we can fabricate a nanopore of the desired size by controlling the ion beam via penetrating ion beam measurements. The smallest aperture thus created was circular with diameter of 30 nm.